Novel protein serine/threonine phosphatases: variety is the spice of life.

The dephosphorylation of proteins on serine and threonine residues is a major mechanism of cellular regulation. Many novel protein serine/threonine phosphatases in the PPP family have recently been discovered and the insights that have been gained into their different functions are summarised in this review.

Interaction with protein phosphatase 1 Is essential for bifocal function during the morphogenesis of the Drosophila compound eye.

The gene bifocal (bif), required for photoreceptor morphogenesis in the Drosophila compound eye, encodes a protein that is shown to interact with protein phosphatase 1 (PP1) using the yeast two-hybrid system. Complex formation between Bif and PP1 is supported by coprecipitation of the two proteins. Residues 992 to 995 (RVQF) in the carboxy-terminal region of Bif, which conform to the consensus PP1-binding motif, are shown to be essential for the interaction of Bif with PP1. The interaction of PP1 with bacterially expressed and endogenous Bif can be disrupted by a synthetic peptide known to block interaction of other regulatory subunits with PP1. Null bif mutants exhibit a rough eye phenotype, disorganized rhabdomeres (light-gathering rhodopsin-rich microvillar membrane structures in the photoreceptor cells) and alterations in the actin cytoskeleton. Expression of wild-type bif transgenes resulted in significant rescue of these abnormalities. In contrast, expression of transgenes encoding the Bif F995A mutant, which disrupts binding to PP1, was unable to rescue any aspect of the bif phenotype. The results indicate that the PP1-Bif interaction is critical for the rescue and that a major function of Bif is to target PP1c to a specific subcellular location. The role of the PP1-Bif complex in modulating the organization of the actin cytoskeleton underlying the rhabdomeres is discussed.

Association of a protein phosphatase 1 activity with the human factor C1 (HCF) complex.

We have screened a human cDNA expression library with a digoxygenin-labelled protein phosphatase 1 (PP1) probe to identify novel PP1 interacting proteins. Eleven cDNA clones were isolated, which included genes encoding two previously characterised and six novel PP1 binding proteins. Three of the cDNAs encoded a protein called host cell factor (HCF), which is an essential component of the cellular complex required for the transcription of the herpes simplex virus (HSV) immediate-early (IE) genes. We demonstrate that HCF and PP1 exist as a complex in nuclear extracts and that this complex is distinct from the form of HCF that associates with HSV VP16. The data suggest novel roles for HCF and PP1, which may be relevant to their functions in transcription and cell cycle progression.

Protein phosphatase X has been highly conserved during mammalian evolution.

Complementary DNA encoding human protein phosphatase X (PPX, also designated PPP4 in the human genome nomenclature) was isolated from a teratocarcinoma library. The deduced amino acid sequence of human PPX differs from that of rabbit PPX in only two in 307 amino acids, demonstrating that the structure of PPX has been highly conserved during the course of mammalian evolution.

Drosophila protein phosphatase 5 is encoded by a single gene that is most highly expressed during embryonic development.

A putative Drosophila melanogaster homologue of mammalian PP5, termed Dm PP5, was identified from cDNA. Dm PP5 comprises a phosphatase catalytic domain preceded by an amino terminal domain containing three tetratricopeptide repeat motifs and shares 60% overall amino acid identity with human PP5. Genomic restriction analysis identified a single Dm PP5 gene that was mapped to the third chromosome at locus 85E10-12 and a strain carrying a deletion that encompasses this gene was identified. Dm PP5 mRNA and protein are more highly expressed in the embryo than at later developmental stages, but their expression levels do not always change synchronously. Dm PP5 protein localises to both the nucleus and the cytoplasm of cells at the periphery of newly cellularized embryos.

Sequence of human protein serine/threonine phosphatase 1 gamma and localization of the gene (PPP1CC) encoding it to chromosome bands 12q24.1-q24.2.

Complementary DNA encoding a catalytic subunit of protein phosphatase 1, termed PP1 gamma, was isolated from a human teratocarcinoma library. The sequence suggests that alternative splicing produces two forms of PP1 gamma, designated PP1 gamma 1 and PP1 gamma 2, which differ in their C-termini. The gene for human PP1 gamma (PPP1CC) was localized to chromosome 12 by analysis of somatic cell hybrid DNA and mapped to bands q24.1-q24.2 by in situ hybridisation. These data show that although PP1 gamma 1 and PP1 gamma 2 are 94% and 93% identical to PP1 alpha respectively, the PP1 gamma gene is not closely linked to the PP1 alpha gene, which has been mapped to chromosome 11.

Isolation of a cDNA likely to encode a novel Ca2+-dependent/calmodulin-stimulated protein phosphatase.

Complementary DNA encoding a novel protein phosphatase catalytic subunit has been isolated from a rabbit brain library. The deduced protein sequence is more similar to the major Ca2+-dependent/calmodulin-stimulated protein phosphatase (2B) in brain (55% identity) than to protein phosphatases 1 and 2A (38-39% identity). A putative calmodulin-binding domain is present C-terminal to the catalytic domain, which closely resembles that of the mouse brain enzyme. These findings represent the first indication that at least two distinct Ca2+-dependent/calmodulin-stimulated protein phosphatases are present in mammalian brain.

Identification of a third alternatively spliced cDNA encoding the catalytic subunit of protein phosphatase 2B beta.

Complementary DNA coding for a catalytic subunit of protein phosphatase 2B was isolated from a human teratocarcinoma library. It encodes a third isoform of protein phosphatase 2B beta, and differs from the cDNA for the second isoform by a deletion of 30 base pairs in the coding region. The deletion results in the loss of ten amino acids between the putative calmodulin site and a postulated autoinhibitory domain. An identical deletion occurs in one of the two alternatively spliced isoforms of PP2B alpha.

Mammalian protein serine/threonine phosphatase 2C: cDNA cloning and comparative analysis of amino acid sequences.

Complementary DNA encoding rat protein phosphatase 2C alpha was obtained from a liver library and used to isolate the homologous cDNAs from rabbit liver and human teratocarcinoma libraries. The amino acid sequences of the three enzymes deduced from the cDNA (382 amino acids) were extremely similar (greater than 99% identity), the maximum number of differences (between rat and human) being four. Amino acid sequences of peptides corresponding to 238 residues (61%) of the protein phosphatase 2C beta isoform from rabbit skeletal muscle were determined and showed 12 differences from the recently published sequence of the rat liver enzyme deduced from the cDNA (95% identity).

Cloning of a novel testis specific protein serine/threonine phosphatase, PPN 58A, from Drosophila melanogaster.

A gene encoding a novel member of the PPP family of protein serine/threonine phosphatases, termed PPN 58A, was cloned from Drosophila melanogaster. The deduced amino acid sequence of PPN 58A exhibits 59-62% identity to D. melanogaster PP1 isoforms, 51% identity to D. melanogaster PPY 55A and < or = 40% identity to other members of the PPP family. The single copy gene PPN 58A maps to chromosome 2 locus 58A. Analysis of PPN 58A mRNA reveals that, like PPY 55A, PPN 58A is a testis specific enzyme.

Protein phosphatase 2Bw and protein phosphatase Z are Saccharomyces cerevisiae enzymes.

cDNAs encoding three protein phosphatases, termed PP2Bw (Da Cruz e Silva, E.F. and Cohen, P.T.W. (1989) Biochim. Biophys. Acta 1009, 293-296), PPZ1 and PPZ2 that have been isolated from a Clontech 'rabbit brain' library are shown to be Saccharomyces cerevisiae clones. PPZ1 and PPZ2 are two novel yeast phosphatases showing 93% amino acid sequence identity to one another. PPZ1 shows approx. 60% sequence identity to S. cerevisiae or mammalian PP1 and approx. 40% identity to S. cerevisiae or mammalian PP2A. These and other observations suggest that the two isoforms of PPZ have functions distinct from those of PP1.

Localisation of the gene encoding the catalytic gamma subunit of phosphorylase kinase to human chromosome bands 7p12-q21.

Skeletal muscle phosphorylase kinase has the structure (alpha beta gamma delta)4 where the alpha and beta subunits are regulatory components, the gamma subunit possesses catalytic activity and the delta subunit is identical to the calcium binding protein calmodulin. A rabbit skeletal muscle cDNA for the gamma subunit has been used to map the human gene (PYKG1) to 7p12-q21, by analysis of somatic cell hybrids and in situ hybridisation. The data suggest that the skeletal muscle gamma subunit gene is located just above the centromere of chromosome 7, with further cross-hybridising sequences at 7q21 and 11p11-14. The liver gamma subunit is distinct and its mRNA does not cross-hybridize with the skeletal muscle gamma subunit cDNA. These results indicate that autosomal human phosphorylase kinase deficiencies affecting both liver and muscle are likely to be caused by a defect in the autosomally determined beta subunit, rather than the gamma subunit.

The major type-1 protein phosphatase catalytic subunits are the same gene products in rabbit skeletal muscle and rabbit liver.

The catalytic subunit of protein phosphatase-1 (PP1) isolated from rabbit liver had the same electrophoretic mobility as, and yielded peptide maps identical to those of the 33 kDa form of rabbit skeletal muscle PP1. The predicted amino-acid sequences of PP1 obtained from three rabbit liver cDNA clones were identical to that of PP1 alpha from rabbit skeletal muscle. These findings suggest that the distinctive substrate specificities and regulatory properties of hepatic and skeletal muscle type-1 protein phosphatases are not conferred by the catalytic subunits themselves, but by regulatory subunits that are complexed to the catalytic subunits in vivo.

Three genes for protein phosphatase 1 map to different human chromosomes: sequence, expression and gene localisation of protein serine/threonine phosphatase 1 beta (PPP1CB).

Complementary DNA encoding a catalytic subunit of protein phosphatase 1, termed PP1 beta, was isolated from a human teratocarcinoma library. Hybridisation with different cDNA fragments showed that all human tissues examined contained 3.1 kb, 4.0 kb and 5.4 kb PP1 beta mRNAs arising from alternative splicing of the 3' noncoding region. The level of the 5.4 kb mRNA relative to the 3.1 kb mRNA was higher in skeletal muscle than in other tissues and the PP1 beta/PP1 alpha mRNA ratio in rabbit tissues was highest in skeletal muscle. The 3' noncoding region of PP1 beta showed extreme conservation (> or = 90% identity) between man and rodents over 1.7 kb, suggesting that this region is of functional importance. The gene for human PP1 beta (PPP1CB) was localised to chromosome 2 by analysis of somatic cell hybrid DNA and mapped to band q23 by fluorescence in situ hybridization. These data show that the genes for three protein phosphatase catalytic subunits PP1 alpha, PP1 beta, PP1 gamma are all located on different chromosomes.

Sequence of the human glycogen-associated regulatory subunit of type 1 protein phosphatase and analysis of its coding region and mRNA level in muscle from patients with NIDDM.

Impaired insulin-stimulated glycogen synthesis of peripheral tissues is a characteristic feature of many patients with non-insulin-dependent diabetes mellitus (NIDDM) and their first-degree relatives with normal glucose tolerance, suggesting putative inherited defects in this metabolic pathway. In previous studies, we have failed to reveal mutations in the coding regions of the muscle-specific glycogen synthase gene and the three genes that encode the catalytic subunits of protein phosphatase 1 (PP1) as frequent causes of insulin resistance. Because the glycogen-associated regulatory subunit of protein phosphatase 1 (PP1 G-subunit) plays a key role in the insulin stimulation of glycogen synthesis and the activity of PP1 is decreased in insulin-resistant subjects, we have now cloned the human G-subunit cDNA to search for abnormalities in the corresponding gene (designated PPP1R3 in the human genome nomenclature) in patients with NIDDM. The human cDNA was isolated from a skeletal muscle cDNA library and was found to encode a 126-kDa protein, which shows 73% amino acid identity to the rabbit PP1 G-subunit. The human G-subunit cDNA from 30 insulin-resistant NIDDM patients was analyzed for genetic variations in the G-subunit by using single-stranded conformation polymorphism (SSCP) scanning of reversely transcribed mRNA. One variant SSCP profile was detected in the region encoding the COOH-terminal part of the PP1 G-subunit in only one NIDDM patient, and subsequent nucleotide sequencing showed a C to A transversion on one allele at base position 2792. This change predicts an amino acid substitution from alanine to glutamic acid.(ABSTRACT TRUNCATED AT 250 WORDS)

A common variant in PPP1R3 associated with insulin resistance and type 2 diabetes.

Selected candidate genes have been analyzed in the Pima Indians of Arizona based on evidence that insulin resistance and type 2 diabetes have significant genetic determinants. An amino acid substitution at codon 905 of the glycogen-targeting subunit of type 1 protein phosphatase that regulates skeletal muscle glycogenesis was recently reported to be associated with changes in insulin action in Danish subjects. In addition to the variant at 905, we report here a novel substitution at codon 883 and common variant of an "ATTTA" element in the 3'-untranslated region (UTR) of the corresponding gene (PPP1R3). The 3'-UTR variant resembled the mRNA-destabilizing AT(AU)-rich elements (AREs) and resulted in a 10-fold difference in reporter mRNA half-life, was correlated with PPP1R3 transcript and protein concentrations in vivo, and was associated with insulin resistance and type 2 diabetes in the Pimas. The variant is more common in Pimas (0.56) than in Caucasians (0.40). Because of its apparent effect on expression of PPP1R3, it may, in part, contribute to the higher prevalence of type 2 diabetes in this Native American population.

Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate.

Protein phosphatase 1 (PP1) is a serine/threonine protein phosphatase that is essential in regulating diverse cellular processes. Here we report the crystal structure of the catalytic subunit of human PP1 gamma 1 and its complex with tungstate at 2.5 A resolution. The anomalous scattering from tungstate was used in a multiple wavelength anomalous dispersion experiment to derive crystallographic phase information. The protein adopts a single domain with a novel fold, distinct from that of the protein tyrosine phosphatases. A di-nuclear ion centre consisting of Mn2+ and Fe2+ is situated at the catalytic site that binds the phosphate moiety of the substrate. Proton-induced X-ray emission spectroscopy was used to identify the nature of the ions bound to the enzyme. The structural data indicate that dephosphorylation is catalysed in a single step by a metal-activated water molecule. This contrasts with other phosphatases, including protein tyrosine phosphatases, acid and alkaline phosphatases which form phosphoryl-enzyme intermediates. The structure of PP1 provides insight into the molecular mechanism for substrate recognition, enzyme regulation and inhibition of this enzyme by toxins and tumour promoters and a basis for understanding the expanding family of related phosphatases which include PP2A and PP2B (calcineurin).

Human immunodeficiency virus disease-related neutropenia and the risk of hospitalization for bacterial infection.

BACKGROUND: Neutropenia is common in patients with human immunodeficiency virus (HIV) disease. However, the degree of risk for serious bacterial infections associated with various levels of neutropenia in patients with HIV disease is not well defined. METHODS: A retrospective analysis of databases containing demographic information for patients attending the San Francisco General Hospital HIV outpatient clinic, test results reported by the hospital's clinical laboratory, and the San Francisco General Hospital inpatient International Classification of Diseases, Ninth Revision (ICD-9) hospital discharge diagnosis codes from October 1, 1992, through November 30, 1993. Risk window time periods were defined, encompassing dates that consecutive absolute neutrophil counts (ANCs) occurred in a single ANC stratum. One risk window at the lowest ANC stratum for each patient was analyzed for hospitalizations with ICD-9 codes indicating bacterial infections. A 5% random sample of medical records was reviewed for end point validation. RESULTS: Codes from ICD-9 had 98% and 96% positive and negative predictive values, respectively, for meeting National Institute of Allergy and Infectious Diseases Division of AIDS [acquired immunodeficiency syndrome] clinical trial end point definitions for bacterial infections. Among 2047 evaluable patients, a significant increase in the incidence of hospitalization for serious bacterial infections was observed for those in the ANC strata of 500 to 749 X 10(6)/L and below. The 95% confidence intervals for the incidence of hospitalization associated with each ANC stratum below 500 X 10(6)/L did not overlap with that for any stratum of 750 X 10(6)/L or higher (22-117 vs 0.4-19 patient hospitalizations per 10000 days at risk, respectively). A multivariate analysis revealed only the severity and duration of neutropenia and black race to be significant end point predictors. CONCLUSION: Among 2047 patients with HIV disease, significantly higher risks of hospitalization for bacterial infections were associated with ANCs lower than 750 X 10(6)/L, especially for ANCs lower than 500 X 10(6)/L.

HIV RNA and CD4 cell count response to protease inhibitor therapy in an urban AIDS clinic: response to both initial and salvage therapy.

OBJECTIVE: To determine the HIV RNA and CD4 cell response to both initial and salvage therapy with protease inhibitor-based therapy, and to examine the relationship between the virological response and pre-therapy characteristics. DESIGN: Observational cohort. SETTING: University-based public hospital AIDS clinic. PATIENTS: HIV-infected adults who received at least 16 continuous weeks' therapy with a potent protease inhibitor (indinavir, ritonavir or nelfinavir)-based regimen, and who have had at least 48 weeks of follow-up. MAIN OUTCOME MEASURES: Plasma HIV RNA and CD4 cell count response at week 48 of therapy for patients receiving their first protease inhibitor-containing regimen, and at week 24 of therapy with a salvage regimen. RESULTS: Of the 337 patients analysed, 170 (50.2%) had a successful outcome (HIV RNA <500 copies/ml after 48 weeks of treatment). Independent predictors of virological failure were higher baseline HIV RNA level, lower baseline CD4 cell count and failure to initiate at least one new nucleoside analog simultaneously at the time protease inhibitor therapy was initiated. The risk of failure increased incrementally across most HIV RNA and CD4 cell strata, with significant increases as the HIV RNA increased above 4.5 log10 copies/ml and the CD4 cell count fell below 100 cells/mm3 (P< or =0.01). The CD4 cell count remained above baseline to week 48 in most patients, regardless of the HIV RNA response. Of the 99 patients who experienced virological failure and switched to a salvage regimen, only 22 (22%) achieved an undetectable HIV RNA level 24 weeks after initiating salvage therapy. Independent predictors of failure with salvage therapy included an HIV RNA greater than 4.0 log10 RNA copies/ml at the time of the switch and failure to use a non-nucleoside reverse transcriptase inhibitor (NNRTI) in the salvage regimen. CONCLUSION: Failure of potent protease inhibitor therapy to suppress HIV RNA levels below detectable levels is common in clinical practice, and can often be explained by their suboptimal use. CD4 T cell counts remain above baseline for at least one year in most patients experiencing virological failure. Successful salvage therapy, which was uncommon, was associated with a low plasma HIV RNA at the time of the switch and the use of a new class of antiretroviral agents (NNRTI) in the salvage regimen.

Segments of bacteriophage lambda (orf 221) and phi 80 are homologous to genes coding for mammalian protein phosphatases.

The amino acid sequences of mammalian protein phosphatase 1 and 2A were compared pairwise with every sequence in the National Biomedical Research Foundation protein sequence database using an exhaustive searching programme [Coulson et al., Comp. J. 30 (1987) 420-424]. The N-terminal half of the protein encoded by an open reading frame, orf 221, in bacteriophage lambda (nt 43,224-43,886 in the map of Daniels et al. [in Hendrix et al. (Eds.), Lambda II. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1983, pp. 519-676] shows 35% identity to either protein phosphatase 1 or 2A in this region. If conservative replacements are included the overall homology rises to 49%. A gene in phi 80 also shows 35% identity with the mammalian protein phosphatases. The results indicate that orf 221 of phage lambda and the homologous phi 80 gene may encode protein phosphatases. The possible roles of protein phosphorylation in the propagation of bacteriophage are discussed.